createTargetsFile: A function to generate a targets file given a directory of...

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

Description

This function, when pointed to a directory containing Illumina bead-level files (e.g. txt, idat, locs, tif) will return a simple targets file of the sort expected by beadarray. Note that a user created targets file is likely to be of greater value.

Usage

createTargetsFile(dir = NULL, nochannels = 1, channel1 = "Grn", channel2 = "Red", txtsuff = "txt", imgsuff = "tif", locssuff = "locs", xmlsuff = "xml", verbose = FALSE, special = c("sdf", "fiducial"), ColourConfusionStop = T, metricsflag = "Metrics", metsep = "\t", metricsection = "Section", metricchip = "Matrix")

Arguments

dir	dir: The directory containing the Illumina bead-level files. By default, will search the working directory.
nochannels	nochannels: Does the directory contain 1 or 2 channel arrays? Setting this argument to be null will result in the function making its best guess.
channel1	channel1: The string indicating that files are associated with the first channel (usually Grn).
channel2	channel2: The string indicating that files are associated with the second channel (usually Red).
txtsuff	txtsuff: The suffix of files containing the bead-level intensities (usually txt, but occasionally csv).
imgsuff	imgsuff: The suffix of files containing the images.
locssuff	locssuff: The suffix of files containing the precise bead locations (usually locs).
xmlsuff	xmlsuff: The suffix of files containing the meta-data (usually xml).
verbose	verbose: Determines whether or not the function reports on its progress as it goes along.
special	special: Files with names containing special words (such as fiducial) are ignored.
ColourConfusionStop	ColourConfusionStop: This determines the behaviour of the function if there is a discrepancy between the number of channels specified, and the number apparently present.
metricsflag	codemetricsflag: This gives the key word that can be used to identify metrics files.
metsep	metsep: This gives the cell separator used in the metrics file.
metricsection	metricsection: This gives the column heading used in the metrics file to indicate array section names.
metricchip	metricchip: This gives the column heading used in the metrics file to indicate the chip name.

Details

This function bases its resultant targets file on the files with suffix txtsuff.

Value

This returns a dataframe containing

Author(s)

Andy Lynch

See Also

readIlluminaData()

Examples

#createTargetsFile(verbose=T)

markdunning/beadarray-devel documentation built on May 21, 2019, noon